public class ProteinInferencePreferences extends Object implements Serializable
Constructor and Description |
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ProteinInferencePreferences() |
Modifier and Type | Method and Description |
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boolean |
equals(ProteinInferencePreferences otherProteinInferencePreferences)
Returns true if the objects have identical settings.
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File |
getProteinSequenceDatabase()
Returns the path to the database used.
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String |
getShortDescription()
Returns a short description of the parameters.
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Boolean |
getSimplifyGroups()
Returns a boolean indicating whether the protein groups should be
simplified.
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Boolean |
getSimplifyGroupsEnzymaticity()
Returns a boolean indicating whether the protein groups should be
simplified based on the peptide enzymaticity.
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Boolean |
getSimplifyGroupsEvidence()
Returns a boolean indicating whether the protein groups should be
simplified based on the Uniprot evidence level.
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Boolean |
getSimplifyGroupsScore()
Returns a boolean indicating whether the protein groups should be
simplified based on the PeptideShaker score.
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Boolean |
getSimplifyGroupsUncharacterized()
Returns a boolean indicating whether the protein groups consisting of
uncharacterized proteins.
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void |
setProteinSequenceDatabase(File proteinSequenceDatabase)
Sets the path to the database used.
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void |
setSimplifyGroups(Boolean simplifyProteinGroups)
Sets whether the protein groups should be simplified based on the
PeptideShaker confidence.
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void |
setSimplifyGroupsEnzymaticity(Boolean simplifyGroupsEnzymaticity)
Sets whether the protein groups should be simplified based on the peptide
enzymaticity.
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void |
setSimplifyGroupsEvidence(Boolean simplifyGroupsEvidence)
Sets whether the protein groups should be simplified based on the Uniprot
evidence level.
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void |
setSimplifyGroupsScore(Boolean simplifyGroupsScore)
Sets whether the protein groups should be simplified based on the
PeptideShaker score.
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void |
setSimplifyGroupsUncharacterized(Boolean simplifyGroupsUncharacterized)
Sets whether the protein groups consisting of uncharacterized proteins.
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public File getProteinSequenceDatabase()
public void setProteinSequenceDatabase(File proteinSequenceDatabase)
proteinSequenceDatabase
- the path to the database usedpublic String getShortDescription()
public boolean equals(ProteinInferencePreferences otherProteinInferencePreferences)
otherProteinInferencePreferences
- the ProteinInferencePreferences
to compare topublic Boolean getSimplifyGroups()
public void setSimplifyGroups(Boolean simplifyProteinGroups)
simplifyProteinGroups
- whether the protein groups should be
simplifiedpublic Boolean getSimplifyGroupsScore()
public void setSimplifyGroupsScore(Boolean simplifyGroupsScore)
simplifyGroupsScore
- whether the protein groups should be
simplified based on the PeptideShaker scorepublic Boolean getSimplifyGroupsEvidence()
public void setSimplifyGroupsEvidence(Boolean simplifyGroupsEvidence)
simplifyGroupsEvidence
- whether the protein groups should be
simplified based on the Uniprot evidence levelpublic Boolean getSimplifyGroupsEnzymaticity()
public void setSimplifyGroupsEnzymaticity(Boolean simplifyGroupsEnzymaticity)
simplifyGroupsEnzymaticity
- whether the protein groups should be
simplified based on the peptide enzymaticitypublic Boolean getSimplifyGroupsUncharacterized()
public void setSimplifyGroupsUncharacterized(Boolean simplifyGroupsUncharacterized)
simplifyGroupsUncharacterized
- whether the protein groups
consisting of uncharacterized proteinsCopyright © 2018. All rights reserved.